Skip to main content
Premium Trial:

Request an Annual Quote

In Print: Last Week's Sequencing-Related Papers of Note: Jun 19, 2012


Cooperativity in RNA-protein interactions: global analysis of RNA binding specificity.
Campbell ZT, Bhimsaria D, Valley CT, Rodriguez-Martinez JA, et al.
Cell Rep. 2012 May 31;1(5):570-581.

Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection.
Neuman JA, Isakov O, Shomron N.
Brief Bioinform. 2012 Mar 24. [Epub ahead of print]

Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.
Ragan C, Mowry BJ, Bauer DC.
Nucleic Acids Res. 2012 Jun 16. [Epub ahead of print]

A pipeline for the identification and characterization of chromatin modifications derived from ChIP-seq datasets.
Kaspi A, Ziemann M, Rafehi H, Lazarus R, El-Osta A.
Biochimie. 2012 Jun 12. [Epub ahead of print]

Targeted re-sequencing of the allohexaploid wheat exome.
Winfield MO, Wilkinson PA, Allen AM, Barker GL, et al.
Plant Biotechnol J. 2012 Jun 18. [Epub ahead of print]

Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon.
Houston RD, Davey JW, Bishop SC, Lowe NR, et al.
BMC Genomics. 2012 Jun 15;13(1):244.

RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts.
Anamika K, Gyenis A, Poidevin L, Poch O, Tora L.
PLoS One. 2012;7(6):e38769.

A framework for human microbiome research.
Human Microbiome Project Consortium. Collaborators: Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, et al.
Nature. 2012 Jun 13;486(7402):215-21.

Structure, function and diversity of the healthy human microbiome.
Human Microbiome Project Consortium. Collaborators: Huttenhower C, Gevers D, Knight R, et al.
Nature. 2012 Jun 13;486(7402):207-14.

Adsorption-driven translocation of polymer chain into nanopores.
Yang S, Neimark AV.
J Chem Phys. 2012 Jun 7;136(21):214901.

Normal and compound Poisson approximations for pattern occurrences in NGS reads.
Zhai Z, Reinert G, Song K, Waterman MS, et al.
J Comput Biol. 2012 Jun;19(6):839-54.

HapCompass: A fast cycle basis algorithm for accurate haplotype assembly of sequence data.
Aguiar D, Istrail S.
J Comput Biol. 2012 Jun;19(6):577-90.

A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals.
Labbé RM, Irimia M, Currie KW, Lin A, et al.
Stem Cells. 2012 Jun 13. [Epub ahead of print]

VARIANT: Command line, web service and web interface for fast and accurate functional characterization of variants found by next-generation sequencing.
Medina I, De Maria A, Bleda M, Salavert F, et al.
Nucleic Acids Res. 2012 Jun 11. [Epub ahead of print]

Transcriptome analysis of microRNAs in developing cerebral cortex of rat.
Yao MJ, Chen G, Zhao PP, Lu MH, et al.
BMC Genomics. 2012 Jun 12;13(1):232.

Unzipping kinetics of duplex DNA containing oxidized lesions in an α-hemolysin nanopore.
Jin Q, Fleming AM, Burrows CJ, White HS.
J Am Chem Soc. 2012 Jun 12. [Epub ahead of print]

Repeat associated small RNAs vary among parents and following hybridization in maize.
Barber WT, Zhang W, Win H, Varala KK, et al.
Proc Natl Acad Sci U S A. 2012 Jun 11. [Epub ahead of print]

GenomeRing: alignment visualization based on SuperGenome coordinates.
Herbig A, Jäger G, Battke F, Nieselt K.
Bioinformatics. 2012 Jun 15;28(12):i7-i15.

NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model.
Polishko A, Ponts N, Le Roch KG, Lonardi S.
Bioinformatics. 2012 Jun 15;28(12):i242-i249.

Weighted pooling — practical and cost-effective techniques for pooled high-throughput sequencing.
Golan D, Erlich Y, Rosset S.
Bioinformatics. 2012 Jun 15;28(12):i197-i206.

SEQuel: improving the accuracy of genome assemblies.
Ronen R, Boucher C, Chitsaz H, Pevzner P.
Bioinformatics. 2012 Jun 15;28(12):i188-i196.

Xenome — a tool for classifying reads from xenograft samples.
Conway T, Wazny J, Bromage A, Tymms M, et al.
Bioinformatics. 2012 Jun 15;28(12):i172-i178.

BatMis: A fast algorithm for k-mismatch mapping.
Tennakoon C, Purbojati RW, Sung WK.
Bioinformatics. 2012 Jun 10. [Epub ahead of print]

SAAP-RRBS: Streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.
Sun Z, Baheti S, Middha S, Kanwar R, et al.
Bioinformatics. 2012 Jun 10. [Epub ahead of print]

Length distribution of sequencing by synthesis: fixed flow cycle model.
Kong Y.
Math Biol. 2012 Jun 12. [Epub ahead of print]

Metagenomic microbial community profiling using unique clade-specific marker genes.
Segata N, Waldron L, Ballarini A, Narasimhan V, et al.
Nat Methods. 2012 Jun 10. [Epub ahead of print]

MicroRNA expression profiling of hypothalamic arcuate and paraventricular nuclei from single rats using Illumina sequencing technology.
Amar L, Benoit C, Beaumont G, Vacher CM, et al.
J Neurosci Methods. 2012 Jun 8. [Epub ahead of print]

Integrative analyses for omics data: A Bayesian mixture model to assess the concordance of ChIP-chip and ChIP-seq measurements.
Schäfer M, Lkhagvasuren O, Klein HU, Elling C, et al.
Toxicol Environ Health A. 2012 Apr 15;75(8-10):461-70.

PANDAseq: paired-end assembler for Illumina sequences.
Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD.
BMC Bioinformatics. 2012 Feb 14;13:31.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.